Variant report

Variant	rs62466594
Chromosome Location	chr7:66473105-66473106
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs12531516	0.81[AMR][1000 genomes]
rs12532160	0.81[AMR][1000 genomes]
rs12534156	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12534278	0.81[AMR][1000 genomes]
rs12534327	0.83[ASN][1000 genomes]
rs12535023	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12537353	0.81[AMR][1000 genomes]
rs12537414	0.81[AMR][1000 genomes]
rs12538152	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12538724	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12539604	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12540695	0.81[AMR][1000 genomes]
rs28867847	0.97[ASN][1000 genomes]
rs35448884	0.81[AMR][1000 genomes]
rs4717335	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4717342	0.84[EUR][1000 genomes]
rs4718438	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4718450	0.81[AMR][1000 genomes]
rs62466582	0.81[AMR][1000 genomes]
rs62466584	0.81[AMR][1000 genomes]
rs62466586	0.81[AMR][1000 genomes]
rs62466588	0.81[AMR][1000 genomes]
rs62466589	0.81[AMR][1000 genomes]
rs62466591	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62466592	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62466596	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62466612	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62466613	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62466616	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62466618	0.97[ASN][1000 genomes]
rs62466620	0.94[ASN][1000 genomes]
rs62466625	0.97[ASN][1000 genomes]
rs62466629	0.83[ASN][1000 genomes]
rs62466630	0.83[ASN][1000 genomes]
rs62466632	0.81[AMR][1000 genomes]
rs62466633	0.81[AMR][1000 genomes]
rs62466634	0.81[AMR][1000 genomes]
rs62466635	0.81[AMR][1000 genomes]
rs62466637	0.81[AMR][1000 genomes]
rs62466638	0.81[AMR][1000 genomes]
rs62466639	0.81[AMR][1000 genomes]
rs62466640	0.81[AMR][1000 genomes]
rs62466642	0.81[AMR][1000 genomes]
rs62466657	0.81[AMR][1000 genomes]
rs62466659	0.81[AMR][1000 genomes]
rs62468374	0.81[AMR][1000 genomes]
rs62468375	0.81[AMR][1000 genomes]
rs62468378	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs62468379	0.81[AMR][1000 genomes]
rs62468380	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs62468381	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs62468382	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758118	chr7:66401430-66859253	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv2759535	chr7:66401430-66859253	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv1032575	chr7:66432853-66576034	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62466594	RABGEF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66462200-66482600	Weak transcription	Aorta	Aorta
2	chr7:66462400-66475400	Weak transcription	Colon Smooth Muscle	Colon
3	chr7:66462400-66475800	Weak transcription	Right Ventricle	heart
4	chr7:66462400-66476000	Weak transcription	Colonic Mucosa	Colon
5	chr7:66462400-66476400	Weak transcription	Gastric	stomach
6	chr7:66462400-66478400	Weak transcription	Pancreas	Pancrea
7	chr7:66462400-66479400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr7:66462400-66482200	Weak transcription	Small Intestine	intestine
9	chr7:66462400-66482600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr7:66462400-66490000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:66462400-66496000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr7:66462400-66500200	Weak transcription	Psoas Muscle	Psoas
13	chr7:66462400-66508000	Weak transcription	Stomach Mucosa	stomach
14	chr7:66462600-66474000	Weak transcription	Osteobl	bone
15	chr7:66462600-66474200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr7:66462600-66474200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr7:66462600-66474400	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr7:66462600-66474400	Weak transcription	Brain Anterior Caudate	brain
19	chr7:66462600-66475400	Weak transcription	Brain Hippocampus Middle	brain
20	chr7:66462600-66475800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr7:66462600-66475800	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr7:66462600-66476000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr7:66462600-66476400	Weak transcription	Brain Angular Gyrus	brain
24	chr7:66462600-66476400	Weak transcription	NHLF	lung
25	chr7:66462600-66479000	Weak transcription	Fetal Brain Female	brain
26	chr7:66462600-66479200	Weak transcription	Fetal Kidney	kidney
27	chr7:66462600-66480600	Weak transcription	Rectal Smooth Muscle	rectum
28	chr7:66462600-66482800	Weak transcription	NHEK	skin
29	chr7:66462600-66484600	Weak transcription	HUVEC	blood vessel
30	chr7:66462600-66487600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr7:66462600-66497200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr7:66462800-66474000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr7:66462800-66476000	Weak transcription	Left Ventricle	heart
34	chr7:66462800-66494600	Weak transcription	Esophagus	oesophagus
35	chr7:66463000-66473400	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr7:66463000-66476200	Weak transcription	Brain Substantia Nigra	brain
37	chr7:66463000-66487200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr7:66463000-66507800	Weak transcription	Fetal Brain Male	brain
39	chr7:66463200-66476400	Weak transcription	HepG2	liver
40	chr7:66463200-66482600	Weak transcription	HMEC	breast
41	chr7:66463200-66483000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr7:66463200-66484800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr7:66463200-66487400	Weak transcription	NH-A	brain
44	chr7:66463200-66510000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr7:66464400-66478400	Weak transcription	Spleen	Spleen
46	chr7:66465200-66475800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr7:66465200-66475800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr7:66467000-66475600	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr7:66467000-66480600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr7:66468600-66484400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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